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The black box is present in contour plots, surface plots, or other 3D graph when exported to a WMF or EMF format.  When this file is imported into other programs, the black box sometimes appears. 

This is due to the fact that the 3D graph types are bitmaps in Grapher.  In a metafile format, bitmaps contain multiple "layers".  One of these layers looks all black when the metafile is broken apart.  This is the case when the file is printed to some printers or inserted into some programs.  You can actually see this in Grapher, too.  After exporting the WMF/EMF file, choose File | Import and select the WMF/EMF file.  When prompted to "Break apart metafile", check the box.  The metafile is broken apart upon import and the black box is present.

To correct the problem, you could use a different file format, such as TIF, JPG, or BMP. These are the preferred export formats for exporting of 3D graphs.